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|
module Bio
#
# = bio/appl/psort.rb - PSORT, protein sorting site prediction systems
#
# Copyright:: Copyright (C) 2003-2006
# Mitsuteru C. Nakao <n@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
require 'bio/appl/psort/report'
autoload :FastaFormat, 'bio/db/fasta'
autoload :Command, 'bio/command'
require 'cgi'
require 'uri'
# == A client for PSORT WWW Server
#
# A client for PSORT WWW Server for predicting protein subcellular
# localization.
#
# PSORT family members,
# 1. PSORT
# 2. PSORT II
# 3. iPSORT
# 4. PSORT-B http://psort.org
# 5. WoLF-PSORT
#
# == References
#
# * http://psort.hgc.jp/
#
class PSORT
# a Hash for PSORT official hosts:
# Key value (host)
# ------- -----------------------
# IMSUT psort.ims.u-tokyo.ac.jp
# Okazaki psort.nibb.ac.jp
# Peking srs.pku.edu.cn:8088
ServerURI = {
:IMSUT => {
:PSORT1 => URI.parse("http://psort.hgc.jp/cgi-bin/okumura.pl"),
:PSORT2 => URI.parse("http://psort.hgc.jp/cgi-bin/runpsort.pl") },
:Okazaki => {
:PSORT1 => URI.parse("http://psort.nibb.ac.jp/cgi-bin/okumura.pl"),
:PSORT2 => URI.parse("http://psort.nibb.ac.jp/cgi-bin/runpsort.pl") },
:Peking => {
:PSORT1 => URI.parse("http:///src.pku.edu.cn:8088/cgi-bin/okumura.pl"),
:PSORT2 => URI.parse("http://src.pku.edu.cn:8088/cgi-bin/runpsort.pl") },
}
# = Generic CGI client class
# A generic CGI client class for Bio::PSORT::* classes.
# The class provides an interface for CGI argument processing and output
# report parsing.
#
# == Example
#
# class NewClient < CGIDriver
# def initialize(host, path)
# super(host, path)
# end
# end
# private
# def make_args(query)
# # ...
# end
# def parse_report(output)
# # ...
# end
#
class CGIDriver
# CGI query argument in Hash ({key => value, ...}).
attr_accessor :args
# CGI output raw text
attr_reader :report
# Sets remote host name and cgi path or uri.
#
# == Examples
#
# CGIDriver.new("localhost", "/cgi-bin/psort_www.pl")
#
# CGIDriver.new("http://localhost/cgi-bin/psort_www.pl")
#
# CGIDriver.new(URI.parse("http://localhost/cgi-bin/psort_www.pl"))
#
def initialize(host = '', path = '')
case host.to_s
when /^http:/
uri = host.to_s
else
uri = 'http://' + host + '/' + path
end
@uri = URI.parse(uri)
@args = {}
@report = ''
end
# Executes a CGI ``query'' and returns aReport
def exec(query)
data = make_args(query)
begin
result = nil
Bio::Command.start_http(@uri.host) {|http|
result = http.post(@uri.path, data)
}
@report = result.body
output = parse_report(@report)
end
return output
end
private
# Bio::CGIDriver#make_args. An API skelton.
def make_args(args_hash)
# The routin should be provided in the inherited class
end
# Bio::CGIDriver#parse_report. An API skelton.
def parse_report(result_body)
# The routin should be provided in the inherited class
end
# Erases HTML tags
def erase_html_tags(str)
return str.gsub(/<\S.*?>/, '')
end
# Returns CGI argument text in String (key=value&) from a Hash ({key=>value}).
def args_join(hash, delim = '&')
tmp = []
hash.each do |key, val|
tmp << CGI.escape(key.to_s) + '=' + CGI.escape(val.to_s)
end
return tmp.join(delim) # not ';' but '&' in the psort cgi script.
end
end # class CGIDriver
# = Bio::PSORT::PSORT1
#
# Bio::PSORT::PSORT1 is a wapper class for the original PSORT program.
#
# == Example
#
# serv = Bio::PSORT::PSORT1.imsut
# serv.title = 'Query_title_splited_by_white space'
# serv.exec(seq, false) # seq.class => String
# serv.exec(seq)
# report = serv.exec(Bio::FastaFormat.new(seq))
# report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
#
# == References
#
# 1. Nakai, K. and Kanehisa, M., A knowledge base for predicting protein
# localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).
# [PMID:1478671]
#
class PSORT1
autoload :Report, 'bio/appl/psort/report'
# Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)
# connecting to the IMSUT server.
def self.imsut
self.new(Remote.new(ServerURI[:IMSUT][:PSORT1]))
end
# Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)
# connecting to the NIBB server.
def self.okazaki
self.new(Remote.new(ServerURI[:Okazaki][:PSORT1]))
end
# Returns a PSORT1 CGI Driver object (Bio::PSORT::PSORT1::Remote)
# connecting to the Peking server.
def self.peking
self.new(Remote.new(ServerURI[:Peking][:PSORT1]))
end
# Sets a cgi client (Bio::PSORT::PSORT1::Remote).
#
def initialize(driver, origin = 'yeast', title = 'MYSEQ')
@serv = driver
@origin = origin # Gram-positive bacterium, Gram-negative bacterium,
# yeast, aminal, plant
@title = title
@sequence = ''
end
# An accessor of the origin argument. Default setting is "yeast".
# Usable values:
# 1. Gram-positive bacterium
# 2. Gram-negative bacterium
# 3. yeast
# 4. animal
# 5. plant
attr_accessor :origin
# An accessor of the query sequence argument.
attr_accessor :sequence
# An accessor of the title argument. Default setting is 'MYSEQ'.
# The value is automatically setted if you use a query in
# Bio::FastaFormat.
attr_accessor :title
# Executes the query (faa) and returns an Bio::PSORT::PSORT1::Report.
#
# The ``faa'' argument is acceptable a sequence both in String and in
# Bio::FastaFormat.
#
# If you set the second argument is ``parsing = false'',
# returns ourput text without any parsing.
def exec(faa, parsing = true)
if faa.class == Bio::FastaFormat
@title = faa.entry_id if @title == 'MYSEQ'
@sequence = faa.seq
@serv.args = {'title' => @title, 'origin' => @origin}
@serv.parsing = parsing
return @serv.exec(sequence)
else
self.exec(Bio::FastaFormat.new(faa), parsing)
end
end
# = Bio::PSORT::PSORT1::Remote
# PSORT1 specific CGIDriver.
class Remote < CGIDriver
# Accessor for Bio::PSORT::PSORT1::Remote#origin to contein target domain.
# Taget domains:
# 1. Gram-positive bacterium
# 2. Gram-negative bacterium
# 3. yeast
# 4. animal
# 5. plant
attr_accessor :origin
# Accessor for Bio::POSRT::PSORT1#sequence to contein the query sequence.
attr_accessor :title
# Accessor for Bio::PSORT::PSORT1#title to contain the query title.
attr_accessor :parsing
# Sets remote ``host'' and cgi ``path''.
def initialize(host, path = nil, title = 'MYSEQ', origin = 'yeast')
@title = title
@origin = origin
@parsing = true
super(host, path)
end
private
# Returns parsed CGI argument.
# An API implementation.
def make_args(query)
@args.update({'sequence' => query})
return args_join(@args)
end
# Returns parsed output report.
# An API implementation.
def parse_report(str)
str = erase_html_tags(str)
str = Bio::PSORT::PSORT1::Report.parser(str) if @parsing
return str
end
end # Class Remote
end # class PSORT1
# = Bio::PSORT::PSORT2
# Bio::PSORT::PSORT2 is a wapper class for the original PSORT program.
#
# == Example
#
# serv = Bio::PSORT::PSORT2.imsut
# serv.title = 'Query_title_splited_by_white space'
# serv.exec(seq, false) # seq.class => String
# serv.exec(seq)
# report = serv.exec(Bio::FastaFormat.new(seq))
# report_raw = serv.exec(Bio::FastaFormat.new(seq), false)
#
# == References
# 1. Nakai, K. and Horton, P., PSORT: a program for detecting the sorting
# signals of proteins and predicting their subcellular localization,
# Trends Biochem. Sci, 24(1) 34-35 (1999).
# [PMID:10087920]
class PSORT2
autoload :Report, 'bio/appl/psort/report'
# Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote).
#
# PSORT official hosts:
# key host path
# ------- ----------------------- -------------------- ---------
# IMSUT psort.ims.u-tokyo.ac.jp /cgi-bin/runpsort.pl (default)
# Okazaki psort.nibb.ac.jp /cgi-bin/runpsort.pl
# Peking srs.pku.edu.cn:8088 /cgi-bin/runpsort.pl
def self.remote(host, path = nil)
self.new(Remote.new(host, path))
end
# Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
# connecting to the IMSUT server.
def self.imsut
self.remote(ServerURI[:IMSUT][:PSORT2])
end
# Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
# connecting to the NIBB server.
def self.okazaki
self.remote(ServerURI[:Okazaki][:PSORT2])
end
# Returns a PSORT2 CGI Driver object (Bio::PSORT::PSORT2::Remote)
# connecting to the Peking server.
def self.peking
self.remote(ServerURI[:Peking][:PSORT2])
end
# An accessor of the origin argument.
# Default setting is ``yeast''.
attr_accessor :origin
# An accessor of the title argument. Default setting is ``QUERY''.
# The value is automatically setted if you use a query in
# Bio::FastaFormat.
attr_accessor :title
# Sets a server CGI Driver (Bio::PSORT::PSORT2::Remote).
def initialize(driver, origin = 'yeast')
@serv = driver
@origin = origin
@title = ''
end
# Executes PSORT II prediction and returns Report object
# (Bio::PSORT::PSORT2::Report) if parsing = true.
# Returns PSORT II report in text if parsing = false.
def exec(faa, parsing = true)
if faa.class == Bio::FastaFormat
@title = faa.entry_id if @title == nil
@sequence = faa.seq
@serv.args = {'origin' => @origin, 'title' => @title}
@serv.parsing = parsing
return @serv.exec(@sequence)
else
self.exec(Bio::FastaFormat.new(faa), parsing)
end
end
# = Bio::PSORT::PSORT2::Remote
# PSORT2 specific CGIDriver
class Remote < CGIDriver
# Sets remote ``host'' and cgi ``path''.
def initialize(host, path)
@origin = 'yeast'
super(host, path)
@parsing = true
end
# An accessor of the origin argument.
# Default setting is ``yeast''.
attr_accessor :origin
# An accessor of the output parsing.
# Default setting is ``true''.
attr_accessor :parsing
private
# Returns parsed CGI argument.
# An API implementation.
def make_args(query)
@args.update({'sequence' => query})
return args_join(@args)
end
# Returns parsed output report.
# An API implementation.
def parse_report(str)
str = str.gsub(/\n<hr>/i, Report::BOUNDARY)
str = erase_html_tags(str)
str = Bio::PSORT::PSORT2::Report.parser(str, self.args['title']) if @parsing
return str
end
end # class Remote
end # class PSORT2
class IPSORT
end # class IPSORT
class PSORTB
end # class PSORTB
class WoLF_PSORT
end # class PSORTB
end # class PSORT
end # module Bio
|
